My site will be down for next few days. Is there any way to so that search engines knows about this and don't do any negative action towards reputation and pagerank of website.
I believe that you should return a status of 503 (Service Temporarily Unavailable). This tells the bots that there is a temporary condition.
This, of course, assumes that by down, you mean that the domain is available but the content is not. If, on the other hand, you are not going to have domain availability, I am unsure what the correct course of action would be.